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Fungi","JoF"],"abstract":"<jats:p>Gray leaf spot (GLS) is a major foliar disease of maize caused mainly by Cercospora zeae-maydis and Cercospora zeina. Although both species infect maize, the comparative transcriptional programs between isolates of different species during maize colonization remain largely unknown. We conducted time-course pathogen-focused RNA-seq of one Jilin isolate assigned to each species during colonization of maize B73 under a controlled inoculation system. RNA-seq reads were mapped to the public C. zeae-maydis SCOH1-5 and C. zeina CMW25467 v3 reference genomes for transcript quantification and putative functional annotation. The C. zeae-maydis isolate developed visible symptoms earlier and showed greater pathogen-derived transcript representation at 6 dpi. The C. zeae-maydis isolate expressed slightly more reference-annotated cell wall-degrading enzyme (CWDE)-associated loci than the C. zeina isolate, whereas the numbers of expressed candidate effector-associated loci were similar. The C. zeae-maydis isolate also showed earlier or stronger host-associated induction of several CWDE- and candidate effector-encoding genes. Both isolates showed post-inoculation induction of candidate transcripts related to lipid metabolism, protease-related functions, and cercosporin biosynthesis, while a subset differed between isolates in the timing or magnitude of expression. RT-qPCR broadly supported the temporal trends of selected candidates. Together, these results define shared and contrasting transcriptional programs of two isolates of different Cercospora species during maize colonization.<\/jats:p>","DOI":"10.3390\/jof12090650","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T08:31:13Z","timestamp":1788251473000},"page":"650","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Time-Course\u00a0Comparative Transcriptomics Between Isolates of Cercospora zeae-maydis and Cercospora zeina During Maize Infection"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-6320-2320","authenticated-orcid":false,"given":"Zhaoreng","family":"Li","sequence":"first","affiliation":[{"name":"College of Plant Protection, Jilin Agricultural University, Changchun 130118, 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